Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 14

1.

Automated ensemble assembly and validation of microbial genomes.

Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM.

BMC Bioinformatics. 2014 May 3;15(1):126. doi: 10.1186/1471-2105-15-126.

PMID:
24884846
[PubMed - in process]
Free PMC Article
2.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.

Genome Biol. 2013 Jan 15;14(1):R2. [Epub ahead of print]

PMID:
23320958
[PubMed - as supplied by publisher]
Free PMC Article
3.

Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone.

Treangen TJ, Phillippy AM.

Genome Biol. 2012 Dec 27;13(12):181. [Epub ahead of print]

PMID:
23270611
[PubMed - as supplied by publisher]
Free PMC Article
4.

Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S.

PLoS One. 2012;7(6):e37919. doi: 10.1371/journal.pone.0037919. Epub 2012 Jun 4.

PMID:
22675498
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA.

Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Erratum in: Genome Res. 2012 Jun;22(6):1196.

PMID:
22147368
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Repetitive DNA and next-generation sequencing: computational challenges and solutions.

Treangen TJ, Salzberg SL.

Nat Rev Genet. 2011 Nov 29;13(1):36-46. doi: 10.1038/nrg3117. Review. Erratum in: Nat Rev Genet. 2012 Feb;13(2):146.

PMID:
22124482
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Bambus 2: scaffolding metagenomes.

Koren S, Treangen TJ, Pop M.

Bioinformatics. 2011 Nov 1;27(21):2964-71. doi: 10.1093/bioinformatics/btr520. Epub 2011 Sep 16.

PMID:
21926123
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Next generation sequence assembly with AMOS.

Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M.

Curr Protoc Bioinformatics. 2011 Mar;Chapter 11:Unit 11.8. doi: 10.1002/0471250953.bi1108s33.

PMID:
21400694
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.

Treangen TJ, Rocha EP.

PLoS Genet. 2011 Jan 27;7(1):e1001284. doi: 10.1371/journal.pgen.1001284.

PMID:
21298028
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A novel heuristic for local multiple alignment of interspersed DNA repeats.

Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):180-9. doi: 10.1109/TCBB.2009.9.

PMID:
19407343
[PubMed - indexed for MEDLINE]
11.

Genesis, effects and fates of repeats in prokaryotic genomes.

Treangen TJ, Abraham AL, Touchon M, Rocha EP.

FEMS Microbiol Rev. 2009 May;33(3):539-71. Review.

PMID:
19396957
[PubMed - indexed for MEDLINE]
12.

The impact of the neisserial DNA uptake sequences on genome evolution and stability.

Treangen TJ, Ambur OH, Tonjum T, Rocha EP.

Genome Biol. 2008;9(3):R60. doi: 10.1186/gb-2008-9-3-r60. Epub 2008 Mar 26.

PMID:
18366792
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Analyzing patterns of microbial evolution using the mauve genome alignment system.

Darling AE, Treangen TJ, Messeguer X, Perna NT.

Methods Mol Biol. 2007;396:135-52.

PMID:
18025691
[PubMed - indexed for MEDLINE]
14.

M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.

Treangen TJ, Messeguer X.

BMC Bioinformatics. 2006 Oct 5;7:433.

PMID:
17022809
[PubMed - indexed for MEDLINE]
Free PMC Article

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Loading ...
Write to the Help Desk